Crew member of the RV Weatherbird II hauls in water samples containing microbes from the Sargasso Sea.Photo courtesy BBSR.

Craig Venter is bringing genomics to the world’s oceans. With the same brash, unconventional style that characterized his efforts to sequence the human genome, he has set out on a global expedition to gather microbes from the world’s oceans and sequence their DNA.

Today, Venter and his colleagues announce the first fruits of this project. They have sampled and cataloged microbes in the Sargasso Sea off Bermuda and put them in a public database online for use by researchers worldwide. Their findings are published today in Science.

In the Sargasso Sea, they found 1800 species of microbes, including 150 new species of bacteria, and over 1.2 million new genes. Although they don’t know what most of these genes do, the research is a first step to understanding more about life in the Sargasso Sea and the larger ocean.

Venter and his colleagues at the Institute for Biological and Energy Alternatives (IBEA) in Rockville, Maryland, which Venter heads, collaborated with scientists at the Bermuda Biological Station for Research, the University of Southern California, and The Institute for Genomic Research, also in Rockville, Maryland.

The sheer number of genes they found in these samples from the Sargasso is astounding and suggests that the microbial life in the ocean is far more abundant and diverse than expected.

“The total number of genes they found is mind-boggling,” says Paul Falkowski of Rutgers University in New Brunswick, New Jersey, who wrote an accompanying perspective in Science.

Sorcerer II Expedition

The Sargasso research was a pilot study for Venter’s current global voyage. He and researchers at IBEA have converted Venter’s 95-foot sailboat called Sorcerer II into a research vessel equipped for an 18-month worldwide scientific expedition. The water samples they collect from such far-flung places as the Galapagos Islands, Panama, and Australia will be filtered and sent to Maryland, where the microbes will be sequenced and put into a database online.

The project and its goals are ambitious. Venter wants to contribute important new knowledge for finding solutions to energy problems, and he says the oceans are the perfect spot on earth to start looking for potential solutions.

They hope to find unique genes or microbes that could create alternative sources of energy or clean up the environment. In theory, a novel gene could, for example, help scientists engineer microbes to make clean fuels such as hydrogen.

The data gathered on the Sargasso Expedition is only a start. The analysis and interpretation will continue for years, providing the basis for future experiments. And, Venter hopes, the findings will stimulate research by IBEA and other scientists who will add to the catalogue of the world’s microbial species.

The world’s oceans are largely unexplored. Microorganisms make up most of the life on this planet, and yet, because many of them cannot be grown in the laboratory, little is known about them.

Gene sequencing holds the potential for unlocking the secrets of the ocean’s microbial treasures. Microbes need not be alive for scientists to sequence their DNA and find their genes. By knowing about the microbes’ genes, we may be able to learn what they do.

Venter is not the first to sequence the genes of microbes from the ocean. For instance, Edward DeLong at Monterey Bay Aquarium Research Institute in Moss Landing, California , is a pioneer in the field and discovered new genes from bacteria in Monterey Bay.

Venter is the first to do it on such a large and ambitious scale.

It’s a new era in genomics. The technology to sequence thousands of microbes is available. The cost of sequencing is coming down and the machines to do the work are available. Also, Venter enjoys rocking the boat. If something seems a little risky, that makes it all the more appealing. He’s a scientist, and he’s also an explorer, a sailor, and adventurer.

The Sorcerer II Expedition is reminiscent of Charles Darwin’s journeys of the H.M.S. Beagle and the H.M.S. Challenger in the nineteenth century. Sorcerer II researchers are out to collect and catalog new forms of life. But unlike Darwin, they will classify the species they encounter not by their appearance but by their unique DNA and genes.

The expedition is funded by the J. Craig Venter Science Foundation, the Discovery Channel Quest Program, and the U.S. Department of Energy. An additional grant from the Department of Energy and a grant from the Gordon and Betty Moore Foundation will be used to pay for sequencing the DNA of the marine microbes.

In the Sargasso Sea, the RV Weatherbird II took water samples from stations 3, 11, and 13. Sorcerer II sampled near Hydrostation “S,” which has been studied for decades.Image courtesy Science.

The Technology

For the Sargasso Sea research and the larger expedition, Venter will use the “shotgun sequencing” method to map the DNA of thousands of microbes from the ocean simultaneously—the same strategy he used on human DNA.

The overall strategy works something like this. Scientists collect ocean water and run the water through filters on the boat. The filter paper containing the microbes is sent to Rockville , Maryland , to be analyzed. Sophisticated computer programs sort the DNA sequences into genes and genomes.

The Sargasso Sea

Venter and his crew embarked on a test study in the Sargasso Sea because they thought it would be a fairly uncomplicated part of the ocean to study. The Sargasso was presumed to be relatively devoid of life because there is not much food in the water.

The Sargasso Sea, which takes its name from the sargassum seaweed that floats on its surface, is a two-million-square-mile body of the water in the middle of the North Atlantic Ocean near Bermuda.

They didn’t have to start from scratch in the Sargasso Sea. Researchers from the Bermuda Biological Station for Research (BBSR), an international hub for oceanography since the early 20th century, have been collecting data in the Sargasso Sea for 50 years.

Two research vessels ferried the scientists to their research sites in the Sargasso Sea. One boat is the RV Weatherbird II, a 115-foot ocean research vessel from BBSR. The other is Sorcerer II. They collected 200-liter samples of water from a handful of locations off the coast of Bermuda in February and May 2003.

“No one has been able to get to the diversity issue of microorganisms in the Sargasso Sea until samples were collected and analyzed by Craig’s group,” says Anthony H. Knap of the Bermuda Biological Station for Research.

What’s in the Sargasso Sea?

Among the findings, the paper’s authors were surprised to discover over 700 genes that they suspect help bacteria capture energy from the sun. This is hundreds more than have been found before, and IBEA researchers want to study these genes further to explore the possibility of producing hydrogen as a fuel source.

Until a few years ago, scientists did not know that these genes, called rhodopsins, even existed in bacteria or that bacteria could collect energy from the sun in this way. Human eyes have a similar kind of receptor that helps us detect light.

Most of the microbes in the Sargasso Sea fell into a handful of categories. These included two kinds of bacteria called Burkholderia and Shewanella oneidensis. Researchers were surprised to find these bacteria because they typically live on land or in nutrient-rich water.

They also found Prochlorococcus bacteria that are abundant in water all over the world. There were bacteria called SAR86—a type of microbe thought to be abundant in the ocean. And they discovered a new species of Archaea, an ancient domain of life that is separate from animals, plants, and bacteria.

Challenges

Pulling out whole genomes of organisms from the collective DNA of an entire community of microbes posed some obvious challenges. For example, it was difficult to distinguish between the DNA sequences of closely related microorganisms.

Researchers were able to pull out only two or three nearly complete genomes, and these were the most abundant organisms in the sample. The nature of the sequencing technique is that rare organisms are less likely to be sequenced, but further sequencing and other techniques could help uncover these microbes.

Genomics gives the first glimpse of what is in the surface waters of the Sargasso Sea. The researchers admit that they are still “a long way from understanding the biology of these organisms.”

“This is only one leg of a stool,” Falkowski says of the study. “Without physical and basic microbiology, genomics cannot answer all the questions we need to know in terms of the microbes that make up the ocean.”

In the end, the Sargasso data raise far more questions than they answer. What else in the ocean don’t we know about? Are there many more genes in marine organisms than we ever imagined? Have we missed the major players in the ocean’s energy cycles?

Much like the human genome project, answers to the tangible, complex, nitty-gritty questions of the ocean and its life forms will only be answered with more research and time.